Contacts of the strand formed by residues 27 - 42 (chain A) in PDB entry 3U8M
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.6 31.4 - - + -
20A PRO* 3.8 11.2 - - + +
21A THR* 3.8 20.0 - - - +
25A ARG 3.6 0.8 + - - -
26A PRO* 1.3 69.5 - - - +
28A ALA* 1.3 61.0 + - - +
29A VAL* 3.3 9.6 + - + +
58A TRP* 4.1 24.9 - - + -
59A SER* 4.2 14.1 - - - +
82A TRP* 4.2 16.8 - - + -
149A GLU 2.7 11.4 + - - +
150A ILE* 3.6 4.3 - - + -
151A SER 3.0 22.4 + - - +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO 3.3 5.4 + - - +
27A VAL* 1.3 72.6 - - - +
29A VAL* 1.3 62.0 + - - +
30A SER* 4.0 1.1 + - - -
57A THR* 3.6 8.8 - - - +
58A TRP* 3.9 11.6 - - - +
59A SER 4.7 1.2 + - - -
151A SER* 3.5 15.9 - - - +
153A ASP* 5.7 2.5 - - + +
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 3.9 15.9 - - + +
28A ALA* 1.3 74.6 - - - +
30A SER* 1.3 65.5 + - - +
31A VAL* 4.0 11.6 + - + -
56A THR* 3.8 27.6 - - + -
57A THR 3.4 5.4 - - - +
58A TRP* 4.4 4.0 - - + -
84A PRO* 4.0 24.7 - - + -
86A LEU* 4.2 5.4 - - + -
150A ILE* 3.9 23.1 - - + -
151A SER 2.7 12.7 + - - +
152A VAL* 3.2 9.0 - - + -
153A ASP* 2.8 27.2 + - - +
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Residues in contact with SER 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA 4.0 1.6 + - - -
29A VAL* 1.3 74.1 - - - +
31A VAL* 1.3 61.8 + - - +
55A GLN 3.4 1.5 - - - +
56A THR* 3.3 8.3 - - - +
57A THR* 2.8 53.9 + - - +
153A ASP* 3.2 12.0 + - - +
154A PRO 4.2 3.1 + - - -
155A THR* 3.3 30.1 - - - +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.1 8.7 - - + +
30A SER* 1.3 78.7 - - - +
32A SER* 1.3 69.6 + - - +
33A LEU* 4.7 2.0 - - + -
54A GLN* 4.4 15.7 - - + -
55A GLN 3.4 5.8 - - - +
56A THR* 4.9 0.4 - - - +
86A LEU* 3.7 31.4 - - + -
140A ILE* 4.4 24.0 - - + +
152A VAL* 4.4 18.4 - - + -
153A ASP 2.9 8.2 + - - +
154A PRO* 3.5 13.3 - - - +
155A THR* 4.5 0.9 - - - -
178A GLN* 3.4 13.2 - - - +
195A VAL* 4.7 15.6 - - + +
197A VAL* 6.0 1.7 - - + +
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 1.3 74.9 - - - +
33A LEU* 1.3 68.4 + - - +
34A LYS* 3.4 21.0 + - - +
53A TRP 3.6 0.2 - - - +
55A GLN* 3.0 47.2 + - - +
155A THR* 2.9 31.2 + - - -
178A GLN* 4.0 15.7 + - - +
197A VAL* 5.9 0.7 - - - -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 4.7 2.9 - - + -
32A SER* 1.3 82.4 + - - +
34A LYS* 1.3 64.8 + - - +
35A PHE* 3.8 37.1 + - + -
52A PHE* 3.6 33.9 - - + -
53A TRP 3.6 0.9 - - - -
54A GLN* 3.9 12.1 - - + -
138A ILE* 4.3 15.5 - - + -
140A ILE* 3.8 31.0 - - + -
176A VAL* 5.1 3.5 - - - +
178A GLN* 3.7 11.6 + - - +
197A VAL* 4.0 26.5 - - + -
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER* 3.4 23.2 + - - +
33A LEU* 1.3 74.5 - - - +
35A PHE* 1.3 65.8 + - - +
36A ILE* 3.5 4.5 - - - +
52A PHE* 3.3 1.3 - - - -
53A TRP* 2.8 55.5 + - + +
55A GLN* 3.6 28.8 + - + +
114A MET* 4.7 6.1 - - - -
155A THR* 4.9 5.5 + - - -
160A ASP 5.8 4.3 - - - +
161A ASP 5.5 3.4 - - - +
164A TYR* 4.0 35.2 - - + -
186E SER* 5.9 5.8 - - - -
187E CYS* 5.6 3.8 - - - +
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.8 29.6 + - + -
34A LYS* 1.3 71.8 - - - +
36A ILE* 1.3 63.9 + - - +
37A ASN 5.0 0.7 - - - +
38A ILE* 5.7 1.1 - - + -
50A VAL* 3.5 32.1 - - + -
51A VAL 3.9 1.6 - - - +
52A PHE* 4.1 10.1 - + + -
138A ILE* 4.1 14.1 - - + -
161A ASP 4.6 10.9 + - - +
164A TYR* 3.8 1.9 + - - +
165A PHE* 3.5 27.0 + - + +
173A ILE* 3.7 19.3 - - + -
176A VAL* 4.1 17.9 - - + -
197A VAL* 4.0 21.1 - - + -
199A LEU* 3.8 46.7 - - + -
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Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS 3.5 18.6 - - - +
35A PHE* 1.3 73.9 - - - +
37A ASN* 1.3 65.7 + - + +
51A VAL* 2.8 25.9 + - + +
52A PHE* 3.9 1.1 - - - -
53A TRP* 3.5 42.2 - - + +
116A SER* 5.6 0.4 - - - +
164A TYR* 3.6 37.7 - - + +
165A PHE* 3.5 4.3 - - - -
166A SER* 2.8 32.2 + - - +
89E TYR 4.6 14.1 - - - +
90E ASN* 6.0 1.8 - - - -
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Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 5.4 0.2 - - - -
36A ILE* 1.3 85.4 - - + +
38A ILE* 1.3 86.5 + - - +
39A LEU* 3.6 19.3 - - + +
50A VAL* 3.6 3.8 - - - +
51A VAL* 2.9 38.3 + - + +
165A PHE* 3.5 8.1 - - - -
166A SER* 3.5 14.9 + - - -
169A SER* 3.1 21.5 + - - +
92E ILE* 4.6 3.8 - - + +
122E SER* 2.9 37.6 + - - -
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 5.7 1.1 - - + -
37A ASN* 1.3 85.6 + - - +
39A LEU* 1.3 62.1 + - - +
41A VAL* 3.8 28.9 - - + -
48A VAL* 5.2 1.8 - - + -
49A ASP 3.7 9.0 - - - +
50A VAL* 4.7 11.4 - - + +
165A PHE* 3.8 20.2 - - + -
169A SER* 3.2 18.6 + - - +
170A ARG 4.8 1.0 + - - -
171A PHE* 3.5 24.2 - - + -
173A ILE* 4.9 2.7 - - + -
199A LEU* 4.0 21.1 - - + -
201A PHE* 3.5 39.5 - - + -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASN* 3.6 35.7 - - + +
38A ILE* 1.3 76.2 - - - +
40A GLU* 1.3 62.4 + - - +
49A ASP* 2.8 18.9 + - + +
51A VAL* 3.9 16.6 - - + -
118A ARG* 3.2 50.0 - - - +
170A ARG* 3.3 18.1 + - - -
171A PHE* 4.8 0.7 - - - -
45E THR* 5.0 2.1 - - - +
47E GLU* 3.8 27.7 - - + +
92E ILE* 3.8 23.6 - - + -
122E SER* 5.0 1.3 - - - -
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Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.9 1.0 - - - +
39A LEU* 1.3 84.0 - - + +
41A VAL* 1.3 73.0 + - - +
42A ASN* 5.0 10.3 + - - +
47A GLU 3.9 1.4 - - - +
48A VAL* 3.6 2.8 - - - -
49A ASP* 3.0 39.9 + - + +
118A ARG* 5.7 2.0 - - - +
120A ARG* 5.9 2.8 - - - -
170A ARG* 4.2 8.7 - - - +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.8 11.4 - - + -
40A GLU* 1.3 85.3 - - - +
42A ASN* 1.3 68.1 + - - +
43A GLU 4.4 0.9 - - - +
47A GLU 3.7 3.6 - - - -
48A VAL* 4.0 8.3 - - + -
125A VAL* 3.2 29.4 - - + -
128A VAL* 4.2 15.9 - - + -
170A ARG* 4.8 1.8 - - - +
171A PHE* 3.5 34.9 - - + -
201A PHE* 3.7 18.4 - - + -
203A LYS* 4.9 8.9 + - - +
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Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLU* 5.0 10.3 + - - +
41A VAL* 1.3 78.9 - - - +
43A GLU* 1.3 58.7 + - - +
44A ILE* 2.9 24.9 + - - +
45A THR* 2.9 36.5 + - - +
46A ASN* 2.8 31.2 + - - -
47A GLU* 2.9 17.0 + - + +
125A VAL* 4.1 1.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il